molecular biology - If inhibiting S6 kinase decreases protein translation, then could inhibiting S6 kinase could possibly slow down long-term potentiation in neurons?

I can't rule it out, but it sounds a lot like trying to tune a piano with sledgehammer.

Neuronal LTP depends on protein translation, but so does absolutely everything else in the cell. Inhibiting protein synthesis at the ribosome will block the formation of all proteins, not just the ones responsible for LTP. Unless there's a link I don't know about between LTP and total levels of protein translation, you're really going to want to look into inhibiting the production of proteins specifically responsible for LTP and not protein synthesis in general.

homework - To understand why satellite cells are genetically inactive in Barr body

DAPI (4',6-diamidino-2-phenylindole) preferentially binds AT-rich DNA (although it binds CG-rich DNA, too), which can give chromosomes distinctive banding patterns if they are polytene or in metaphase. In interphase condensed chromosomes, such as the inactive X chromosomes of female mammals (Barr Body), the relatively high concentration of tightly-packed DNA makes the chromosome appear as a brighter spot in the nucleus. When the DNA of a chromosome is decondensed (such as the rest of the chromosomes in interphase), it appears as more-or-less homogeneously stained DNA in the nucleus.

A great picture is here (see below), A is the DAPI staining, B is a protein localized to the Barr Body, C is the RNA (Xist) which binds the Barr Body.

Since the active X is not condensed, it appears as do the rest of the chromosomes, so cannot be identified among the mixture of autosomes. The difference in DAPI appearance has nothing to do with activity per se, but rather differences in how tightly packaged the chromosomes are.

I do not understand the first part of your question, though. You cannot tell from a still image that the Barr Body is relatively inactive. If your were doing experiments on live cells, you could measure RNA production (using a labeled nucleotide), immunofluorescence to show localization of e.g. RNA Polymerase, or reporter genes located on the inactive versus active X chromosomes. If you clarify your question, I can answer better.

molecular biology - What is the mechanism of transgene integration (from expression vector to the host genome)?

What is your host in this case? For integration into the genome of a bacterium, you would need to use an "integration" vector. Most commercial vectors (such as pUC18) will be maintained without integrating into the host genome.

Here is a description of an integration vector from the Bacillus Genetic Stock Center to give you an idea of how foreign DNA would be integrated into a Bacillus genome:

Integration vectors are plasmids that feature conditional replication
coupled with a selectable marker. If the plasmid is transformed into
an appropriate host under conditions that select for the plasmid’s
presence but restrict its replication, all transformants will have
integrated the plasmid into their chromosome (or some other resident
DNA capable of replicating under the selective conditions). In
practice, the selectable marker usually specifies antibiotic
resistance. Conditional replication usually means that the plasmid has
replication functions that work in E. coli but not in gram-positive
bacteria, such as B. subtilis. Sometimes a temperature-sensitive
replication phenotype is employed instead. Integration is targeted to
a particular locus on the chromosome by including identical sequences
on the plasmid. If there is a single homologous sequence, a single
crossover will integrate the entire chromosome into the target locus
by a Campbell-type mechanism. If there are two homologous sequences,
and they are relatively close together on the chromosome, then a
double crossover will result in a cassette integrating between the
chromosomal targets. (source)

For most routine molecular biology labwork, there is no need to integrate genes into the E. coli genome. Integration is usually used to generate "knockout" cell lines to study gene function in the bacteria of interest.

botany - Photosynthetic Pigments vs. Chloroplasts

Photosynthetic pigments are the chemicals which take part in photosynthesis, in particular they are they ones which absorb photons and fluoresce (emit photons of a different wavelength) or emit electrons. Pigments are molecules, and chlorophyll is a key example. These pigments are required for photosynthesis to take place, as they generate the electrons which create the electrochemical gradients which power photosynthesis, thus all photosynthetic organisms will have photosynthetic pigments of some kind.

Chloroplasts are membrane-bound organelles in plant cells, made up of many hundreds of thousands of molecules including pigments. Plant photosynthesis takes place on their internal membrane, the thylakoid. Specifically, the thylakoid membrane of chloroplasts is the membrane across which the aforementioned electrochemical gradients are created in plants.

Chloroplasts originated from a free-living bacterium, probably a cyanobacterium, entering a eukaryotic cell. So prokaryotes don't have them because the chloroplast endosymbiosis event was one way in which plants diverged from their non-plant ancestors. So you can think of a cyanobacterium as a free-living chloroplast - they have their own internal membranes similar to the thylakoid across which electrochemical gradients are created for photosynthesis. Conversely, you can think of a chloroplast as a small cyanobacterium living symbiotically inside a plant cell.

biochemistry - Can scientists create totally synthetic life?

In principle it is possible. Life doesn’t contain some divine or intrinsically spiritual element that we would have to add to our artificial organism potion to breathe life into it. At this moment we are limited by gaps in our knowledge and by the current state of technology.

We first have to better understand fundamental principles of life on a multi-level scale: from quantum mechanics, through biochemistry, structural biology, molecular evolution, to macroscopic function and behavior on the organism level. This, together with development of enabling technologies, will require decades of research but some steps have already been taken.

One of the promising approaches is re-writing, as exemplified in this work:

We redesign the genome of a natural biological system, bacteriophage T7, in order to specify an engineered surrogate that, if viable, would be easier to study and extend. (...) The resulting chimeric genome encodes a viable bacteriophage that appears to maintain key features of the original while being simpler to model and easier to manipulate. The viability of our initial design suggests that the genomes encoding natural biological systems can be systematically redesigned and built anew in service of scientific understanding or human intention.

or a minimal cell synthesis project:

Construction of a chemical system capable of replication and evolution, fed only by small molecule nutrients, is now conceivable. This could be achieved by stepwise integration of decades of work on the reconstitution of DNA, RNA and protein syntheses from pure components. (...) Completion would yield a functionally and structurally understood self-replicating biosystem. (...) Our proposed minimal genome is 113 kbp long and contains 151 genes. We detail building blocks already in place and major hurdles to overcome for completion.

So, technically it’s very difficult but definitely can be done, which is really exciting.

transcription - Why does the T7 RNA Polymerase require a reducing environment ie. DTT

A quick search on T7 cysteines gave some clues:

Bacteriophage T7-induced DNA polymerase is composed of a 1: 1
complex of phage-induced gene 5 protein and Escherichia coli
thioredoxin. Preparation of active subunits in the absence of
sulfhydryl reagents indicates the reduced form of thioredoxin is
sufficient for formation of the active holoenzyme. The oxidized
form of thioredoxin, thioredoxin modified at one active site
sulfhydryl by iodoacetate or methyl iodide, or thioredoxin modified
at both active site sulfhydryls by N-ethylmaleimide, are all
inactive, being defective in complex formation with gene 5
protein.

Adler and Modrich, J Biol Chem 258:6956 (1983)

There's a more recent paper (Aguirre et al, Inorganic Chemistry 48:4425 (2009)) that mentions the "the enzyme critical sulfhydryl cysteine groups", but unfortunately I only have access to the abstract.

Update: It seems to be an old finding, rather than a rationale concerning the cytoplasmic redox state. According to Chamberlin and Ring, JBC 248:2235 (1973),

General Requirements-The general requirements for T7 RNA
synthesis directed by T7 DNA polymerase are shown in Table
I. As expected for a template directed polymerase, RNA
synthesis shows an absolute requirement for DNA, the 4
ribonucleoside triphosphates and Mg++.

(no surprises there ;)

The activity of the
enzyme is reduced significantly if a sulfhydryl reducing
agent such as b-mercapto-ethanol is omitted from the
reaction. The addition of 10^-5 M p-hydroxymercuribenzoate to
the assay system in the absence of b-mercaptoethanol
abolished all activity, indicating that the enzyme contains a
sulfhydryl group necessary for activity.

However, if you see the table I, the remaining activity after removing bme is still 74%

There seems to be 7 exposed cysteines (Mukherjee et al, Cell 110:81 (2002)), but I could not find any paper discussing their roles.

biochemistry - What does the human body use oxygen for besides the final electron acceptor in the electron transport chain?

Another small addition

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There is class of oxidoreductases called oxygenases which incorporate molecular oxygen into the substrates and not just use it as an electron acceptor like in oxidases (note that the terminal enzyme in ETC is an oxidase and there are other such oxidases). In other words, oxygen is not a cofactor but a co-substrate. Oxygenases are further classified into dioxygenases and monooxygenases which incorporate two oxygen atoms and one oxygen atom respectively. Examples:

• Cytochrome P450 family (monooxygenease): involved in detoxification of xenobiotics


• Cyclooxygenase (dioxygenase): involved in production of prostaglandins which are involved in pain and inflammation. Many NSAID painkillers like aspirin, paracetamol and ibuprofen target cyclooxygenase-2 (COX2)


• Lipoxygenase (dioxygenase): Involved in production of leukotrienes which are involved in inflammation.


• Monoamine oxidase (monooxygenase): Involved in catabolism of neurotransmitters such as epinephrine, norepinephrine and dopamine.

Does oxygen deprivation result in death just due to the halting of ATP
production, or is there some other reason as well?

Death predominantly occurs because of halt in ATP production. Some cells such as neurons (and also perhaps cardiac muscles) are highly sensitive to loss of oxygen (for energy requirements) and clinical death because of hypoxia usually occurs because of loss basic brain function.

What percentage of the oxygen we take in through respiration is
expelled later through the breath as carbon dioxide?

As already mentioned, it is said that there is a rough 1:1 ratio of CO₂ production and O₂ consumption. However, as indicated in a comment by CurtF, O₂ does not form CO₂; it forms water in the last reaction of ETC. CO₂ is produced in other reactions of Krebs cycle.

Glycolysis produces 32 molecules of ATP for 1 molecule of glucose via ETC (see here). There are three complexes in ETC and the third is dependent on oxygen; so you can assume that 1/2 a molecule of O₂ consumed for production of 3 ATP molecules. Therefore 32 molecules of ATP would consume 4 molecules of O₂. Seems like there is a 1:1 ratio of CO₂ production and O₂ consumption.

We can see it like this:

FADH₂ enters ETC at the second complex whereas NADH enters at the first. We can say that as long as NADH is present FADH₂ would not require an extra oxygen.

An NADH or a FADH₂ molecule would require 1/2 molecule of O₂. There are 8 molecules of NADH and 2 molecules of FADH₂ produced during glycolysis+krebs cycle which would require 10/2 = 5 molecules of O₂. Glycolysis produces 4 molecules of CO₂ during krebs cycle.

However, 2 cytosolic NADH molecules require 2 ATPs (in other words another NADH molecule) to be transported to mitochondria. So the net effect may be actually close to 1:1 O₂:CO₂.

Another factor to keep in consideration is that the three complexes do not actually produce ATP; they just pump proton to create a chemical potential. The F₀F₁-ATP synthase would probably work only after a threshold of H⁺ potential is established. The 1 ATP molecule per complex is most likely to be the mean value and not exactly what really happens per reaction.